@arsus5478 The maintainer must update the dependencies for the package.

the info line contains the answer:

Info: applications using this runtime: io.github.Hexchat

You need to remove Hexchat if you want to remove the end-of-life runtimes it requires.

I regret to inform you that the maintainer wrote in February 2024: This will be the last release I make of HexChat. The project has largely been unmaintained for years now and nobody else stepped up to do that work.

My computer uses both system and user remotes.

Because my .var directory is almost full, [...]

If you're low on disk space you probably want to have everything installed as either user or system, to avoid having some runtimes installed in both.

Wait is hexchat really dead? Didn't it replace xchat? So what's the go to irc client now?

anything I've ever removed with ( flatpak remove --unused ) has not re-appeared again. Not that I've noticed anyway.

not related to the problem, but if space is an issue convert your file system to btrfs. you get on-the-fly compression and (more important) deduping, so two same files occupy space only once.